Previous studies suggest that structure and reactivity of soot depend on combustion conditions like the fuel/oxygen ratio and nature of fuels. However, the essence of how combustion conditions affect physical and chemical properties of soot is still an open question. In this study, soot samples were prepared by combusting toluene, n-hexane, and decane under controlled conditions, and their hydrophilic properties, morphology, microstructure, content of volatile organic compounds, and functional groups were characterized. The hydrophilicity of n-hexane and decane flame soot increased with decreasing fuel/oxygen ratio, while it almost did not change for toluene flame soot. Fuel/oxygen ratio had little effect on the morphology of aggregates and the graphite crystallite size. The primary particle size and the content of volatile organic compounds on soot decreased with decreasing fuel/oxygen ratio. Less hydrophobic groups (C-H) and more hydrophilic groups (C=O) were observed on lean n-hexane and decane flame soot than that on the corresponding rich Volatile organic compounds had little effect on the hydrophilicity of soot while the hydrophilicity correlated linearly with the ratio of C=O content to C-H content. The hydrophilic functional groups were found to be mainly located at graphene layer edges and on surface graphene layers in soot.